A New Implicit Solvent Model for Brownian Dynamics Simulation: Solvent-Accessible Surface Area Dependent Effective Charge Model
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- ANDO Tadashi
- Department of Biological Science and Technology
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- MEGURO Toshiyuki
- Department of Biological Science and Technology
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- YAMATO Ichiro
- Department of Biological Science and Technology
Bibliographic Information
- Other Title
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- ブラウン動力学シミュレーションのための新規溶媒効果モデル:露出表面積依存型有効電荷モデル
- New Implicit Solvent Model for Brownian Dynamics Simulation Solvent Accessible Surface Area Dependent Effective Charge Model
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Abstract
A new simple implicit solvent model, effective charge (EC) model, was introduced into the Brownian dynamics algorithm based on AMBER united-atom force field. In the EC model, an atomic charge was decreased as a function of solvent-accessible surface area of the atom. We carried out the Brownian dynamics simulations of a 28-mer ββα fold peptide using four implicit solvent models: a generalized Born/solvent-accessible surface area (GB/SA) model, a solvent-accessible surface area (SA) based solvent model, a SA in combination with distance-dependent dielectric (DD/SA) and the EC combined with DD/SA (DD/SA/EC) model; and the calculated results on structure and dynamics of the peptide were compared with those of molecular dynamics simulation using explicit solvent model. Several artifacts were observed in the simulation using the GB/SA model. On the other hand, simulation using the DD/SA and DD/SA/EC implicit solvent models were free from such artifacts. Especially BD with the DD/SA/EC model gave the most stable trajectory as judged by root mean square deviations from the initial structure without large computational cost.
Journal
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- Journal of Computer Chemistry, Japan
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Journal of Computer Chemistry, Japan 3 (4), 129-136, 2004
Society of Computer Chemistry, Japan
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Keywords
Details 詳細情報について
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- CRID
- 1390001205180653696
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- NII Article ID
- 130000056836
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- NII Book ID
- AA11657986
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- COI
- 1:CAS:528:DC%2BD2MXmt1OgsA%3D%3D
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- ISSN
- 13473824
- 13471767
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- NDL BIB ID
- 7194700
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- Text Lang
- en
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- Data Source
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- JaLC
- NDL
- Crossref
- CiNii Articles
- KAKEN
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- Abstract License Flag
- Disallowed